CRIT/workflow
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==Transcription Factor Example== | ==Transcription Factor Example== | ||
| + | |||
| + | ===Motivation and Problem Set up | ||
| + | |||
| + | Cis regulatory elements as a means of regulating gene expression have | ||
| + | been extensively studied. However, beyond such motifs, are there | ||
| + | inherent properties of the targets themselves that make them more or | ||
| + | less likely to be regulated by a given class of transcription factors? | ||
| + | As an example, do essential transcription factors preferentially | ||
| + | regulate essential targets? Are there genome composition features | ||
| + | such as GC or codon bias that influence which targets are regulated by | ||
| + | which TFs? | ||
===Input Data=== | ===Input Data=== | ||
| + | Here, we use three different datasets as shown. | ||
[[File:schema.png|200px|thumb|left|Data Input Set up]] | [[File:schema.png|200px|thumb|left|Data Input Set up]] | ||
| + | |||
| + | These objects are named as follows in the R dataset. | ||
| + | (1) T: Transcription factors and their associated properties | ||
| + | |||
| + | (2) C: Connector Matrix matching transcription factors to their associated targets | ||
| + | |||
| + | (3) G: Gene targets and their associated properties | ||
Revision as of 14:42, 29 January 2011
Transcription Factor Example
===Motivation and Problem Set up
Cis regulatory elements as a means of regulating gene expression have been extensively studied. However, beyond such motifs, are there inherent properties of the targets themselves that make them more or less likely to be regulated by a given class of transcription factors? As an example, do essential transcription factors preferentially regulate essential targets? Are there genome composition features such as GC or codon bias that influence which targets are regulated by which TFs?
Input Data
Here, we use three different datasets as shown.
These objects are named as follows in the R dataset. (1) T: Transcription factors and their associated properties
(2) C: Connector Matrix matching transcription factors to their associated targets
(3) G: Gene targets and their associated properties
